Different As It Always Will Be
by YAY Productions
Summary: Physical and mental torture has left Donatello struggling with his sanity. Leonardo has to make a call in bargaining with a devil disguised as an angel, but Raphael will move heaven & hell. Michelangelo gives up his fun self to be the strong one at any cost. Meanwhile, one of Splinter's sons is trying to kill him. The future will never be the same as it never was. /SAINW Origins/
1. Donatello: The Soldier of Death

_**Different As It Always Will Be**_

 _ **Phase I:**_

 _ **Chapter One:**_ _ **The Soldier of Death**_

* * *

The cold darkness of the cell was a great relief to him. Nothing could be more welcoming at this point. He rested back, his shell propped in the corner, not a single ounce of light entering his eyes. Sometimes he did not know if they were closed or open in the pitch black, but he was okay with that. The thought of the glare that so often permeated his sight was enough to make him choke though, his hands shaking as he attempted to wrap them around his legs. His raw, bare skin was torn, and he could feel the warmth of the blood dripping ever so cautiously down his face, arms, and torso. His toes curled to the best of their ability, the memory of the shocking still so recent. The shocking, he finally surmised, was worse than the cutting. His durability to throwing stars, katana blades, sais, and nunchaku had grown thick, but the electricity still reached down into his core. The seizures were also growing worse though. Silently, he wished that the drowning feeling would last long enough that he would suffocate. He had passed out many times, especially in the beginning, but now his body was fighting against that too.

Donatello desperately wished that it wouldn't.

His mind wavered, exhaustion overcoming him. While before he tried to get as much rest as possible, now his care for sleep had left. He knew well after studying the Russian experiments that a sleep deprived person will go crazy, and then promptly perish. Although he already felt like he was out of his mind, the last part appealed to him.

Death? Death was the one friend that would never visit.

Shifting ever so slightly, Donatello stifled a moan. No broken bones today, which he guessed was a good thing. For now anyways. If they were easier on him this time, they were probably going to be more difficult tomorrow. Hopefully he wouldn't have to jump through the hoops. But he would prefer the hoops over the table...if they tried to shove one more probe down his throat or up his...well, he wished they understood the concept of anesthesia. He was too weak to struggle at this moment, but tomorrow? He was going to try and take as many with him as possible. He did not care how unmanly it was to go kicking and screaming- it was his only avenue to take out his anger sometimes.

His thoughts seemed to go blank as the pain in his chest began to erupt again. Leaning his head back, Donatello gasped, clenching his teeth ever so tightly. How many times had he nearly bitten off his own tongue? How many times had he hoped to choke on his own fluids? To let the poison drip into him, to let it take him away? Why couldn't he just will himself into the next world?

And yet he continued to fight. Not for his own sake, no. Only because he knew what they were doing to him. Pushing one's physical boundaries was one thing, but mental manipulation was another. The way they bore his brothers' masks, the way they mimicked their voices. The taunting of his father...the self deprecating tone that would erupt from his own mouth. They were doing everything they could to make him associate his family, and himself, with pain.

His first course of action was to ignore it, but that wore quickly. His attempt to imagine April O'Neil, the ginger that he had been crushing on for well over a year, had turned against him when he called her name out once. Just once, and that was all it took. They knew her, and were using her against him now too. His ability to daydream of days past had been stripped of him, and he could hardly even remember the stench of the sewers he called home. The laboratory that he had locked himself away in so often for so many hours was long forgotten, and the memories of the loving embraces his family would hold him in were long gone. He had no memories except for this existence, as the term life could not describe it. He was down to his last resort, and even now his obsessive chanting was becoming more droll with time. But he could not forget...he could not forget that he was Hamato Donatello. And Hamato Donatello had a family that loved him, even if those thoughts of closeness had left him long ago.

The surges that were wearing down his body had taken their toll. At this point, he knew not why breath remained with him. By ending his life, he would end their attempts. They needed him alive, and he was not going to let them break him.

Standing slowly, Donatello rose, turning around and facing the corner he was in. Closing his eyes softly, he fingered the stone,and braced himself. He took a sharp breath in, and held it.

He could see stars. His head pounded, the shock rattled his body. Grabbing the wall the steady himself, he slammed his skull against it again. He crumpled to the ground, barring his teeth. Again...he could do it again until he couldn't.

As the feeling in his neck tightened, he hoped this time would snap it. Oh...the beauty in dying. He embraced its destruction, clung to its hope. An ending wasn't always bad, and every story had to come to an end. He was ready for this one to end.

Bone cracking chills caressed his body sweetly. He could hear the mocking tones of his brothers, pretending to care as they carried him off into the light. The light was bad, but he was gone. The light couldn't hurt him anymore, and neither could they.

His form was limp, being dragged across the ground. Strange sounds fell onto his near deaf ears, begging for recognition. Commands, a motor roaring, the screams of pain. The screams for him. He wouldn't fall for it this time. They needed to let him die in peace. In his own mangled pain. He was tired of their pretending, he was tired of their abuse.

A familiar smell drenched his nostrils in an overwhelming fog. Only disgusting American, New York sewers smelled quite like that. Only the rushing crash of the manhole cover made that sound. Only the hushed, concerned voices that rose above him could be of his missed family.

A jolting pain shattered his dying meditation, and all he could hear then was his own scream.


	2. Leonardo: The Charge of Brokenness

_**Different As It Always Will Be**_

 _ **Phase I:**_

 _ **Chapter Two:**_ _ **The Charge of Brokenness**_

* * *

He thought the sewer smelled bad. The stench of burning flesh though- that was a real kicker. It wasn't quite like a barbecue, no it was very distinct. The strong aroma was a genuine amalgam of ingredients. Anything from that metallic copper smell that pennies and blood have in common, to charcoal and even sulfurous rotten eggs that have mixed in with pungent, briny water. It was fatty with a biting, acrid tinge to it. But unlike human flesh, this had a fishy undertone to it. Rancid, algae like with scum on top. Basically, like any one of his brothers after they had been shot with a some alien photon phaser what do you call it, and then didn't shower after a week of workouts. It was disgusting.

What terrified Leonardo the most though was the source of the smell. The sealed door could not keep it at bay. Whatever was inside was foul, twisted, and broken. His assumption was that it was an unclean, but frequently used, burden of torment. A torture device that he did not want to see.

Gesturing for Raphael and Michelangelo, they prepared themselves. The sounds coming from within were grotesque, like an animalistic moan and a garbled cry. A broken sob within a mutilated growl. A sharp, piercing sound followed, as if someone was crashing boulders together. The blubbering howl was too much for him to bear. Apparently, his brothers agreed with him without saying a word.

Raphael proceeded to wedge the razor sharp tips of his sais into the airtight crevice. Another shaking and desperate plea erupted from behind the locked doors as they struggled to open the portal to the disturbed soul. Whatever was being done to it, they had to do something. Anything to help bring them a step closer to their brother. Even an inch forward to where Donatello might be.

With an almost satisfying pop and expulsion of compressed air, the forbidden entry opened. The room was so dark shapes could hardly be seen with the naked eye.

And then the figure in the corner moved. Quickly, in a determined succession, hurling itself into the chipped, sharp wall. Like so many others, it was in a trance of sorts, as if possessed. Its one mindset, zombie in nature, was to propel itself once again.

The final crack was nauseating. It crumpled to the ground, unable to move as he rushed over to its gaunt form. Liquid, blood he knew, covered the floor. Bones of the sewer rats it had consumed to survive littered the floor, turning his stomach.

Finally reaching into the abyss, Leonardo and Raphael grabbed him before turning to Mikey, who was standing guard at the door. He could feel the tremors of the poor creature, its feet dragging the ground.

It was Michelangelo who noticed first. Of course he did, he had the advantage of the light. His shaky tone was filled with fear, apprehension, and a shocked exasperation. Leo's eyes finally fell to what now Raph was looking at as well, and his mind could not hardly process it.

Contorted, disfigured, lacerated and maimed. That was only the beginning of the description, the first words that filled his searching and failing intellect. Not one of the three of them could breathe his name, nor utter the now pure and unblinded outrage that coursed through their systems.

It was paralyzing for them to see him this way. It was a strangling sensation, a burning freeze to their steps. They had found so many others like him before, some in worse conditions and some in better, but they had always been looking for him. They had been looking for Donatello. The Donnie they knew, he was six foot tall, lanky but muscular. Strong but inventive, the purple bandana almost always around his face. His eyes, even when troubled, sparkled with an untamed genius. But this...this gargoyle was not Donatello. It was thin, starved. Its eyes were sunken, rolled back into its head and bloodshot. Its skin was scarred, and as he held it, he knew that the suffocating odor was coming from its body. Fresh burns laced its face and arms, the carapace cracked and fractured. One of the legs had been broken before and poorly set definitely a long time ago, no doubt a poor attempt by his brother's fragmented efforts. It was crooked, crippling.

At first they merely glanced at one another, and then the shockingly quiet hallway. In one step, they exited the dungeon, and in less than a millisecond, alarms started blaring. The dim haze of white light turned to flashing colors, predominantly red. His brother had a tracker in him, and they had to figure out where it was and how to get it out.

It was then that Raphael showed the side of himself that was underneath the constant brooding shell. Grabbing Donatello's arm, he pressed it through the door. The alarms stayed, and the unholy music of droids marching drew closer. Raph cursed under his breath, but tried the other arm. It was then that Leo realized what their famed hothead of a brother was doing. It was now or never.

Pressing Donnie's back into the sensor, he noticed no change until the back of his neck snapped backwards. A slight light change, a different warning. He knew where the device was that they could use to follow, tail, and find them.

Right now, their first course of action was to escape. They could outrun the pink, brainy aliens long enough to give them the time they needed to remove whatever they needed to.

Leonardo could only hope that they did not have any other surprises that would try to climb up their shells. They just needed to get their brother home. To be more specific, whatever was left of their brother.

Racing down the corridor, Mikey took the lead, the side, and behind. His unending energy had made them become confident in his defensive skills. He could be everywhere he needed to be, as he so used to remind them when they wound up with a water balloon or cream pie in their face. Raphael had the endurance and strength it would take to get Donnie home safely.

But Leonardo, he had the precision. The decision. And with so much at stake, neither of his once trouble making brothers questioned his commands.

They soared through the air, gliding across the floors with the accuracy of only those of their kind. Ninjas, trained in only the best martial arts.

Somehow Mikey kept the bots away. As Leo exited through the hole they had made to break in, Raphael pushed Donatello out. Picking him up, Leo barely turned back to make sure his younger brothers would make it out. He couldn't sacrifice one of them, not a single one. He couldn't do this again.

And then there they were, at his side. Driving their mishap of a vehicle was Casey Jones, an ally he knew they could trust to be there. He was reckless, a rule breaker, and speedster, but right now that was exactly what they needed. It felt like an eternity passed in seconds as their trip down busy New York roads turned into dark, dank sewer tunnels. Pulling out his smooth, katana , he could do nothing but apologize to the pain he was about to inflict on his brother. Slicing ever so gently as to not damage any more nerves, he flicked the edge of his blade to the underside of the chip. It was not connected to his brother, but merely implanted.

Donatello screamed, the pain reaction very delayed. His wild eyes flickered as Leo quickly removed the bit, crushing it and throwing it out the window. His brother's body flailed violently, and at first they just sat there, unsure of whether to hold him down, or to let him do what he needed to. It didn't matter though, as just as quickly his response was, so was his decline. His poor, naked body collapsed, fresh blood trickling down the back of his neck. If Leo had been any less careful, Donatello's spine would have been severed.

Staring blankly, Leo could not stop the tears from overwhelmingly caress his cheeks. His heart was shattered as he gazed at the still form that lay at his feet. His brother, the genius. His brother, the animal. His brother...fighting a seemingly unending fight.


	3. Michelangelo: The Jester of Sorrow

_**Different As It Always Will Be**_

 _ **Phase I:**_

 _ **Chapter Three**_ _ **:**_ _ **The Jester of Sorrow**_

* * *

The burning sensation around his eyes stung as the tears etched across his face. The taste of salt entered his mouth as the drizzle turned into a flow. Back flips, front flips, cartwheels, and twists made him fly, and the droplets flung themselves around. They were scattered onto the walls and floor as they soared through the air. He had to stay on top of things, protect those he held closest. He couldn't focus on what he had seen. What he was seeing. What he could never erase from his mind.

Donnie had always been the thinnest of the four of them. He spent so much time in his lab, that he often forgot to eat. He had a tough frame though, as Splinter would pull him out by his ears sometimes and make him drink tea and train with the rest of them. Splinter always encouraged their unique gifts, but he believed in balance.

Striking a Kraang in the chest, Mikey pulled away, watching as the nasty, gooey, life force oozed out of it. Alien blood was nasty and disgusting. Phaser beams surrounded him, but he was lucky. It wasn't that the Kraang were bad shots, it was just that they did not inflict enough damage. A shot to the shell was barely noticeable, and as long as it didn't hit you in the face, the pain it would rake across his arms and legs was similar to someone tickling him and pricking him with a punch of needles at the same time. Donnie told them before that it was messing up their nervous-y system or something like that. He always said that it would wear off pretty quickly, and it always did.

Lately though, as Mikey and Raph and Leo had discovered, the Kraang's game had become stronger. The bruises and bouts of paralysis during battle had become more frequent, no doubt a direct result from immediate changes their enemy would make.

As much as he tried to be himself at home though, Mikey found the loss of his best friend and brother disheartening. To top that off with the impossible mission of finding Donatello, and the discovery of other mutants that had been...messed with and experimented on had left Michelangelo the jokester straining to keep a smile for his father and remaining brothers. Even April's hopeful smile had long faded, and Casey's seriousness had evolved into brooding worse than Raph. Leo did nothing but plan and spar with Raph. The temperamental one of the family never slept, but so often would sneak out of the house to reign terror on any hoodlum he could. He got the most tips, including this one. And this time, he was right. Splinter rarely approved of their outings, and instead meditated. His mutant body had been weakening, between stress and the claim he had of a mental connection with Donatello. Mikey didn't know if it was true or not, but it didn't really matter. All he knew was that they had to save his brother. That Donnie's life was at stake, and he would do whatever he had to do to save him. They would work together, be a family again. Everything would be good again. Normal.

At least, as normal as four teenage ninja turtles could get living underneath the city of New York with their sensei and two human friends taking care of other mutants could be.

Guarding Leo, Donnie, and Raph as they crawled out of the breach, he could feel his muscles, as defined as they were, stiffen and freeze. Within minutes, seconds perhaps, he wouldn't be able to move his leg.

Flinching at Raph's firm grasp at his ankle, Mikey could feel himself being pulled out. Standing him up quickly, Raph wrapped his arm around his shoulder, supporting him. Because that was Raphael- the column and cornerstone in the temple of their family. At least, that was how Splinter always put it. He would be hard, and seemingly uncaring at times, but he needed to be.

The van sprang to life as Casey roared the engine. He was their getaway, and he was very good at it. They were sailing down the streets, and Mikey knew sirens would accompany them soon. His leg was jumping all over the place, and his hands were shaking. Raph was massaging his calf, but his mind, like the rest of them, was elsewhere.

Looking up, Mikey did not want to see. He didn't, after all the time he spent in wanting to, look at the mangled corpse of his brother. That's all he looked like. Something dead, no life in him. Blood was caked on his forehead, and his breaths were so shallow, he could hardly notice them. His skin was pale, peeling like a human with really bad sunburn. His nails- oh God- were near gone. They had been ripped out. Whatever was left had blood and dirt crammed under them.

As Casey took a sharp turn into the entrance of the sewers, Leo drew his katana. Mikey did not understand what he was doing, but Raph seemed to acknowledge. His heart nearly stopped as Leo drew the blade through Donnie's spine. His body started twitching, and Mikey did not want to look. Just in the nick of time, Leo pulled something from the bloody mess.

The scream that Donnie let out was nothing he had ever heard before today. It was the same sound that he heard outside of his brother's cell, magnified tenfold. Donnie was thrashing, convulsing with spasms. His warm, brown eyes were a dark red, his pupils so dilated Mikey thought he would be blind.

As Casey slammed on the brakes, Mikey flew forward. Donnie was still once again. He still trembled though, but Mikey dare not touch him. He would have to find the best way to bring comfort to his brother.

As Raph yanked him back up in the sitting position, Mikey glanced over to Leo. He was squeezing his fist until a very satifying crunch was heard. Kicking the window open slightly, Raph nodded as Leo threw out whatever it was. It didn't matter to MIkey. He trusted that they caught on to something he did not.

Settling on the terrifying view in front of him, he wished they could get home soon. It was taking far too long, and even though he would never admit it to anyone else, he was afraid. He was afraid of what happened to Donnie. He was afraid of what Donnie would do next. He was afraid of what Leo would do, or Raph. He was afraid of what was happening to his own body, but the tremors were starting to slow at least.

Casey braked abruptly, and Mikey tried to stand. The door had swung open, and April's sob made him grind his teeth. He had to think of this as a victory. This was not a loss, they had not lost anyone. They had won.

They had won. They had won their brother back.


	4. Raphael: The Cornerstone of Fear

_**Different As It Always Will Be**_

 _ **Phase I:**_

 _ **Chapter Four:**_ _ **The Cornerstone of Fear**_

* * *

Peering back into the hole, he watched his brother beginning to crumple. He reached through, grasping ahold of his leg, and yanked him down to the ground. He did not care for one second that he was going to hurt Mikey as he dragged him over metal and gravel, because he knew that the Kraang would do far worse things to him if they could get their tentacles on him. He had seen it with his own eyes. There had been so many, with so few coming out alive. If he turned around, he would see the latest damage done to his family.

Pulling his brother up sharply, Raphael wrapped Mikey's arm around his neck, practically dragging him behind Leonardo. Swinging his little brother into the van, he nodded at Casey while he revved up the engine. They were breaking the speed limit before he even had the door closed. They were streaking down the streets, but he knew they were being followed. As much as he had tinkered with this old rust bucket, he knew it could not outrun alien technology.

Adrenalin was coursing through his veins with such a ferocity that he didn't realize he was grinding his teeth until his jaw popped. All he wanted to do was place his head between his knees and try not to vomit, but he had more important priorities. His first prerogative, as simple and stupid as it seemed, was to stabilize Mikey. He couldn't do much for his other brother, laying there stone cold. The first aid kit that he was so fluent with, even in helping the others before him, was useless yet again. He had seen worse- that was for sure. But many of those in better condition than this had died, and there was nothing he could do about. As much of a brute he was, he had become fluent in medical care, much like his family. In this profession, it was necessary. All the heavy equipment was back home in the medical bay. He couldn't count how many bodies he had seen seize up like the one in front of him, or how many first stage mutants literally just fell apart into the same jelly that Timothy was made of. They couldn't handle it. The bleeding, butchered carcasses of the Kraang's experimentation. The ones that starved while they were feeding them because they were so malnourished, or the ones that ate themselves to death. So few had even lived, and even then, he questioned some of their sanity. There was nothing left of their home but a refuge for the strange, odd, quirky, or dejected. The battered and broken. It was so hard to think that merely a year and a half ago all he knew were his three brothers and his father. Now they were a sanctuary to mutants and humans alike.

As cruel as it was though, he would trade them all for the being in front of him. It was his fault that his beloved brother had been taken months ago, and it was his fault that the words to describe Donatello were simply indescribable. It was horrifying, but he forced himself to stare as he rubbed the electric shock from Mikey's leg. Leonardo plucked the tracker from him, and as the van slowed- or rather braked several times abruptly- he held onto Mikey to keep him from falling. If only they knew his grief, the blame he put on himself. But his pain was none as what his little brother Donnie must have gone through. Although he had always towered over him, Raphael still looked down at him, in the best brotherly way possible. And now he was nothing but skin and bones. Or bones...because what was left of anything else was melting away. His cheeks were so hollow, his eyes so sunken, his skin so tattered. Raphael may have seen this before, but it was different. Ever since they had found the first mutant that had truly been tortured- Jason, they had realized that they had to become numb, because rattled ninjas were not effective ninjas. Timothy and Garson had been pretty easy to deal with, simply because they were just not that humanoid anymore. But Jason? Jason was just a kid, but the obvious torment was toxic. The kid still had nightmares.

Their finding of him had...shaken them up pretty badly, to say the least. What they hadn't known at the time though, was that it was going to prepare them for everything else. But this? This was unbearable. This was their brother. More importantly, this was his brother.

Casey jumped out the van as April opened the van, no doubt prepared to take care of their injuries, or another mutated freak. They always brought someone back, dead or alive. But the sound she made...oh God...Casey barely caught her before she dropped to the floor. She and Donnie had always been close, but their flirtationship had been cut short. Out of the four of them, he had been her best friend, crushes aside. Splinter was there, ready with Dr. Rockwell. The look in his father's face was odd though- he had known. He had known that Donatello would be with them. He had known that he was going to be this mangled, this...hacked apart. And he was ready. All those years of meditation must have actually done something, for him to know today. For him to have, in Raphael's opinion, wasted time meditating the months while they had been looking for him, and for him to be prepared right now. He knew. He had probably always known.

Donatello was shivering, and as Raphael helped carry him, he knew that his brother did not have long. He was as ice, even in the warmth of the sewer. He didn't even seem to fit in his own shell, which seemed dead from undernourishment. His shell seemed...dead. That concept just swung like a pendulum in Raphael's mind, his throat choking up as he watched the good doctor struggle to even find a vein for an IV. All that he could think was maybe they should just let Donnie go.


	5. Donatello: The Uncertainty of Awareness

_**Different As It Always Will Be**_

 _ **Phase I:**_

 _ **Chapter Five:**_ _ **The Uncertainty of Awareness**_

* * *

Silence. At first that was all Donatello heard. If only one could hear pure and utter silence. It was dangerously beautiful. He could revel in its magnificence, but usually silence was ever so painful as well. Right now sound was not only silent, but pain was as well. And sight, and touch, and smell, and taste. It was all silent. Was he dead? Was it finally over? He wanted to grin, to dance, to leap for joy in his deathness. If this was death, he was in heaven. His heart soared.

He choked suddenly. It was all coming back. Slowly, with his heart soaring and beating in his chest, he was coming back. Darkness began to turn to light before his closed eyes, the smell of alcohol filling his nostrils. He could taste his blood still, he could hear the beeping of the machines. Not the machines...he couldn't move...hey would pierce through him again...the cold metal being left in his flesh. The pain was returning in full force, but stopped. The sounds he heard were ones of anguish, garbled, but familiar. He wanted to reach out, to open his eyes, but they were so heavy. He could barely focus on what he needed to for survival. He had to move, if only to avoid what was coming for a single second. Anything to give him one second of relief. But he could not move. He remembered this...being strapped by the wrists and ankles as they poked and prodded. That was when he had it easy. Before the trials.

A soft hand stroked his face, and he jumped, all of his senses now fully online. His eyes flew open, and he barred his teeth. The light above his head was just blinding as usual, but he would adjust. He twisted his body violently, trying to break his bonds. He knew he was going to tear his wrists again, but he began shouting at the top of his lungs.

"I am going to kill you! Every last rotting piece of you! Do you hear me?! I am going to kill you!" He struggled, snapping his teeth as the hand recoiled. "Let me go! Let me show you what you have made!"

"My son..."

That voice, they were using these tricks again. It was not going to work. He had no hope left, so how could he fall for it? "You learned long ago that I will not go for your ploys..." He brought his voice so low into a snarl that he was almost surprised his voice did not cut out entirely.

The light dimmed, moving to the side, and a face came into view. "My son..." Tears were not just dripping from the face he was staring at, but pouring down. Drop by drop they fell onto his carapace. "My dear, dear son."

Donatello only stared, tense and apprehensive. "Let. Me. Go."

Green hands came up to his wrists, unbuckling the leather shackles that held him down. In the moment they were free, he snapped, not caring that his legs were still bound. He reached for the throat of the body the hands were attached to, staring the robot down. A perfect representation of Raphael. It was disgusting. "Release me," Donatello demanded.

The bot only looked at him, unmoving. Another, similar to Michelangelo, unlatched his feet. In one swift move, Donatello swung a fist straight into the gut of the Kraang bot he was holding onto, leaping towards the other. It backed off, and Donatello ran.

He could only the words, "Let him go," as he raced out the room. Why? What it going to be today? What surprises would he have to endure? A booby trapped maze? They enjoyed testing his intellect alongside his physical form, pushing the boundaries of both.

His feet could not carry him far, but far enough would be fine. His neck ached, his scars ached, his muscles and bones ached. His head ached. But he gasped as he ran into a room that he knew far too well. How could the Kraang have known the lair so well? Were they able to finally use their probes to take all his memories? They had such difficulties in the past with his mutant brain.

Donatello begged for his body to move, but with each step, he began to decelerate. His knees buckled underneath, but before he could hit the floor, someone caught him. "I've got you, Donnie," Leo's voice echoed to him. "And I am _never_ going to let you go," The words were almost gasped out. But how many times had he heard them? How many times had he allowed them to work? How many times had he paid the price? But he was too exhausted to fight back. Surely they would know that. They always got a kick of bringing him just to the edge before giving him enough time to heal within a hair's breadth of living.

Someone came up beside him. It was the Raphael styled one, reluctant, but helpful. They begin carrying him back to the bed, but he knew what they were going to do. If he was in a bed, they were going to use the mutagen. They were going to make his mind nothing more than mud, before bouncing it back to his current state. It had some nasty side effects, but it could be worse. It could be so much worse.

They didn't strap him back in this time. They knew he wasn't going anywhere, their sensors probably proved that. A face mask was attached over his mouth and nostrils, and fresh air flowed, allowing him to breathe. Waiting, waiting for it to be over, he could do nothing but wait as the fresh air filled his lungs. Nothing, nothing, and more nothing. The being beside him was barely out of his peripheral range, but it was too quiet, too unmoving. An occasional hum came from it, but then its towering frame moved towards his direction. He jumped, still waiting. He was disgusted with how perfect they had made his father. More grey in his fur this time, thinner than before, but a direct mockery of his beloved master.

"Donatello, my son. I understand that you cannot comprehend this, but I will prove it to you. You are safe, and you have no need to worry. Over time, you will learn this, but for now, you need to rest. Rest your mind, my son. Rest..." The hand passed over his face, and almost like magic, he closed his eyes, unable to lift them again. His mind, as powerful as it was, found it impossible to function, and he slipped into the welcoming realm of silence and darkness once more. Impossible, was his last thought before succumbing fully to power of the spoken words.


	6. Leonardo: The Unknowing Knowledge

_**Different As It Always Will Be**_

 _ **Phase I:**_

 _ **Chapter Six:**_ ** _The Unknowing Knowledge_**

* * *

"I've got you, Donnie," Leonardo choked at the words. His little brother was so panicked, fighting so hard. "I am never going to let you go," Donnie's eyes were still wild, like a trapped animal. He was struggling to breathe, as if he had asthma, and trying to move, but anything that he had left in him was gone.

Raphael slid up underneath Donnie's other arm, helping Leonardo carry him back to the infirmary. Donnie was practically limp in their arms, wheezing and doing his best to catch his breath.

Together, they gently placed him back on the bed. Raph reached for the straps, but their Master and father placed his hand over his hot headed son's. "No. We saw what happened last time. And I do not think he will be going anywhere else right now," Simply gesturing the others away, Splinter leaned over their exhausted brother, whispering to him.

Slowly, Leonardo backed out of the room, his brothers following suit. Mikey attempted to take a seat on the couch beside Casey and April while Raph paced, but Leo himself did not know what to do. His mind, as trained and skilled as it was, could not understand what had happened. He did not want to say anything, but it was the youngest amongst them that dared to speak.

"Man..." Mikey's voice pierced the silence. "I mean...man..."

Raph huffed, pulling out his sai. "I'm going to kill them. All of 'em!"

Casey jumped up, blind anger in his eyes. "Count me in! We done seen this too many times, but this one is one of our own. Nobody touches one of us!"

Nodding his head, Mikey gripped his nunchaku. "I get first shot."

"Guys..." Leo spoke quietly, his voice cracking as tears began finally welling up. His voice was so low he barely heard himself, and his brothers most certainly did not listen to what he said. "Guys!"

All heads turned towards him as he walked into the center of the room. Eyes peered around the sewer tunnels, eyes of so many of the others that they had helped. Genuine people who were relying on them to keep their cool, even in the hardest situations. "We have to think this out."

"I have!" Raph snarled, plunging his sai into the air. "I'm gonna split them all in half!"

"But that's not our first priority," Leo posed, his arms crossed. "Which is very unfortunate, because I would be first in line to dish out everything that the Kraang deserve. We have to be smart. More smart than ever before. They are not stupid. They play on everything that makes us human, including our emotions. They are probably counting on us storming their front. We can't do that. We don't go into a battle already fighting what we're feeling. We will make mistakes. Right now, we have to be here. We have to be here for each other, for Sensei. For..." Leo's voice cracked. "We have to be here for Donatello. Our brother is home. That is reason enough to celebrate. Only yesterday we questioned if he was still alive. And here he is, sleeping in one of our beds, and not lying on a stone cold floor. Wen he wakes up, he is going to be confused. You heard what he said..."

"He said he wouldn't be fooled again," Mikey replied, his head hanging low. He sat down again, grinding his teeth together. "He thinks we're Kraang."

Raphael growled. "But he wants back at 'em, just like us."

"Then we let him heal. And if he's ready-" Leo was caught off by his brother.

"When he's ready," Raph corrected.

"When he's ready," Leo stated firmly, "We will let him make that choice. But I am not going to lose another brother, or anyone, now that we've got him back. That is not a risk I am willing to take."

Casey grunted, but placed himself beside April again, wrapping his arm around her. "I got you, babe. I sure ain't gonna let them do anything to ya."

Dr. Rockwell stepped out of the room, rubbing his temples. Closing the door quietly behind him, he shook his head.

"What's goin' on, Doc?" Raph snapped his attention to the good man, beating Leo to the question.

"He is...resting, surprisingly enough."

"Will he make it?" April's muffled words were the ones everyone was afraid to say. Leo felt a chill crawl straight up his spine the moment they hit his ears. He didn't want to think about it. Some had come back from worse, others had left from less. It was all a matter of the person. Some that came back did not stay...but chose to leave this world because they could not adjust from what had happened to them. He could not think about that, dare to imagine his precious brother taking a blade to his wrist the same way another had.

Rockwell cringed so softly, Leo was certain he the only one who caught it. "Well...my friends, it is too early to tell that. He is...as stable as he can be right now, but there is not much more I can do at the moment. I am giving him fluids, but I have to manage everything slowly right now. Too much of something good, and his body may reject it," Pausing, he sighed. "Do not hold your breaths for answers. Matters like these take time. But you all know that far too well..."

April nodded, but fresh drops of grief started dripping down her flushed cheeks. Casey held her tight, but Raph stormed off, and headed for the dojo. Leo could only hope that he was going to take a small piece of his anger out on his punching bag, instead of trying to sneak his way out again.

Pulling his legs around him, Mikey sat alone on one corner of the couch. Walking over, Leo put a hand on his shoulder. "It'll be okay, little brother. Everything is going to be okay. You'll see. This is Donnie we're talking about. He always bounced back from late nights in the lab, to training with the rest of us, and running with us on the surface. He can come back from anything."

"He's not Superman, Leo," Mikey shrugged his hand off of him, giving him a mournful look. Getting up, he turned back, gazing at his big brother. "None of us are."


	7. Michelangelo: The Aftermath of Thought

_**Different As It Always Will Be**_

 _ **Phase I**_

 _ **Chapter Seven:**_ ** _The Aftermath of Thought_**

* * *

His heart beating a thousand miles an hour in his chest. No, it had to be closer to a million. Maybe even light speed. Would he blow up if his heart was beating that fast? How fast would his heart have to beat and it kill him? Would he just fall over dead right this second? Would he even know if he died? Would he feel it?

All of these thoughts were pouring through Michelangelo's head. He lifted his head from his knees to see his big brother standing over him. He was doing his best to reassure him, but Leo was doing a lousy job. Mikey was sure he didn't even believe his own words.

But Mikey's response almost surprised himself. "Donnie's not Superman, Leo. None of us are."

Leo looked shocked. It was always Mikey who kept them positive, kept them alive. But right now, the clown of the lot of them couldn't even create a smile. He wanted to be like April, to cry and be comforted, but he couldn't. He was a man, and men did not cry.

That was when he noticed the tear stains on Leo's face. Raph may be the toughest around them, but Mikey already knew he cried. But Leo? He didn't. He would simply meditate, like Splinter. Ever since Donnie had been taken, he had been so much more serious. He had become older.

Well, really they all had. Nobody would probably guess that they weren't even 18 yet. Heck, were they even 17? He didn't even know what the date was. Had their mutation day come and gone already?

Opening his bedroom door, he looked for his calendar. It wouldn't be on the wall, he already knew that much. He tore it down months ago, after crossing off day after day of not finding Donnie.

Underneath a pile of...something, he finally found it. Using a throwing star, he pinned back up, circling the day's date. In a small notation, he wrote the simple words, _Donnie found alive._

Reading it over, Mikey choked. Donnie had been found alive. His brother was alive! He was breathing, and all Mikey had to do was walk over to another room to be able to see him. He may be hooked up to all kinds of wires and gizmos, but he was alive.

There was a soft knock at his door, and Leo walked in. He stared at where Mikey's view was, a small smile forming on his firm lips. "Donnie found alive," He whispered, looking back at his orange banded brother.

Mikey nodded. "It's a win, right Leo?"

"It is a win, Mikey. We found Donnie, and we found him alive."

"And he'll be okay, right Leo?"

Leo was silent, and Mikey could watch as thoughts raced across his big brother's brain. "I...I have to be honest. I don't know. I...I don't know..." Sitting on Mikey's bed, Leo stared at the wall. "I don't know...I hate not knowing..."

Taking his place beside his brother, Mikey pulled his legs in so he could sit Indian style. "So do I."

Leo sighed, but shoulders sinking slightly. He didn't say a word, and Mikey did not feel obligated to say anything either. He knew what Leo was going through, because he was going through it himself. They were more alike than either would probably imagine. They didn't want to be alone, but they needed to think. And Leo's thoughts were far too chaotic for him to meditate. Mikey was almost glad, because sitting with him this quietly felt good.

He didn't want to think. He had no urge to. But his mind wouldn't stop at all the possibilities. He didn't want to think what would happen if Donnie died. He had grieved already, that day he yanked the calendar down. He didn't think they would ever find him. But Raph...Raph was unstoppable. He defied Leo and Splinter's orders, and so often went out with Casey to find something new. And eventually, he did.

Mikey could remember it clearly. The rest of them were meditating with Splinter, and he bust in the dojo holding Donnie's tattered mask. He said it wasn't all there was. He had taken it from Shredder's lair, a gift from the Kraang. One of the Foot he had...interrogated had given him some of the information. That Donatello was alive. But more importantly, the man told Raph where their brother was.

Mikey never asked Raph what he did to that Foot soldier. He, alongside the rest of them, knew that Raph wasn't so stupid to let him go and alert everyone what he knew. Turning him into the police would be stupid, because the Shredder would probably bail him out. So they just opted not to speak about it.

He hadn't believed it. He thought it would be just like any one of their other missions, and he was tired of those. They had emotionally and mentally drained him, after finding so many bodies, failed experiments. He was weary of the mutilated things they would find, alive or not. He was done with opening his home to strangers.

Mikey did not want to be taken the wrong way, not even in his own mind. He believed in what they did. He truly did. But it was a hard life. He almost wished that he and his brothers had never gone up to the surface. But where would they be now? They had halted the Kraang's plans, merely put a pause on what they had in mind. They would have done so much by now, especially since they had saved April that first night. Eventually, they would have been found, and the Kraang would have had far more forces than they could handle. They would have all been captured, but maybe at that point they would have all been killed. Maybe not...tortured. He dared to think the word that he knew his brother had been through. Pure torture.

"We should get a pizza," Leo said almost as if it were a normal day. "Maybe Donnie will want some when he wakes up."

Mikey did not say that he doubted Dr. Rockwell would allow Donnie to have any, but instead agreed. They hadn't had pizza in so long. Pizza was good for any mood, but having one when they were happy was always the best. Maybe it would make them happy. Or at least help...


	8. Raphael: Convulsion of Reflection

_**Different As It Always Will Be**_

 _ **Phase I:**_

 _ **Chapter Eight: Convulsion of Reflection**_

* * *

Blood boiled in his veins as he clutched his sai so tightly that his knuckles started going pale. He could hear the stomps of his footsteps echoing down the tunnels, but he didn't care who he scared. He made his way into the dojo, several of the victims they saved exited. They all knew from experience that if he was in there by himself, they better make way or they might end up his sparring partner...which was a very bad idea.

 _"I am going to kill all of them, do you hear me? All of them! I am going to split them all in half!"_

It was funny in a crude way how quickly he could from wanting to take them all out all by himself, to wanting Donnie to be able to get a shot at the...the things that hurt him the way they had.

 _"He wants back at them! Just like us..."_

Raphael's own words haunted him. He had seen the fight that his brother had put up. He had felt the uncontrollable power right underneath the tight skin that was pulled across his brother's gaunt frame. There was absolutely no restrain in Donnie's words or actions. He just lacked the strength that he used to have. The strength that he would build up again to avenge himself.

His fists met his punching bag hard. The constant pounding with the occasional kick was supposed to him calm down, but it did quite the opposite. He was working himself up, his heart beating faster and faster. Steam was coming off of his head, smoke out of his ears and nose. He was getting angrier and angrier.

"I hate them," He whispered hoarsely. "I hate them. I hate them!" HIs voice grew louder and louder. "I hate them!" He almost screamed.

He heard the crack before he felt it. Raph buckled, clenching his teeth in an effort not to cry out. He hoped he hadn't broken his wrist, and he had received worse injuries during his various battles, but this hurt like fire and brimstone.

Unbinding his wraps, Raph inspected his wrist, trying to move it. It was already starting to swell, and his hands were shaking. It moved slightly though, and he was certain it wasn't as bad as it felt. He walked into the kitchen, and opened the refrigerator to pull out a bag of ice. They kept them stacked out of the mere necessity for them.

"What have you done to yourself?" The sound shocked him, and he jumped. So much for his ninja skills. The lizard tail flicked him, the piercing eyes flickering. "You have to stop doing that."

"Shut up Lisa," Raph growled, not wanting to talk to anyone, meanwhile the feisty new mutant right now.

"Testy, testy," She shook her head as she grew serious, her mouth drawn. "I'm glad you found your brother."

"I don't want to talk about it," Raph closed his eyes.

 _He was shaking, trembling as they pulled him out of that cramped cell. The lights were blaring in their faces, and he wanted to cry. Raph really wanted to cry. It smelled so bad, and Raph could barely hold onto his brother because he was so slick with blood._

"Raph?"

Gazing at the young girl, he was thankful that she hadn't been there long enough to know what the Kraang could have really done. She was one of the firsts that they had collected after the capture of his brother.

Splinter had assumed that the collection had started right before the Kraang took Donatello, but most of it happened afterwards. They only knew that because of the stories the survivors told. They were all victims, but survivors...they were the ones that lived. Raph didn't even know how they took care of them all. He was pretty sure Splinter would take credit cards and run them up, just so that they could feed everybody. So that April and Casey could run to the surface and get the medical supplies they so desperately needed. So that they could survive.

Survive. It was what they had to do. For everything that they had all been through, they had to survive.

"Raphael," The voice was much deeper this time. It was his father.

"Sensei," Raph nodded, not bowing as Leo probably would have.

"Lisa was concerned. You would not answer her after she called out several times. You have been standing here far too long, my son."

"I didn't even notice."

Splinter stroked his beard. "So I can tell. What is troubling you?"

"You know what," Raphael felt like the question was stupid.

"Donatello. Your brother. He is home. When he recovers, we will be celebrating."

"But Sensei-" Raph wheeled around, fire in his eyes. "We have to take out the Kraang! We have to right the wrong!"

Ignoring his son's outburst, Splinter just nodded. "And we will. But right now we have to heal. We all have to heal," Looking at his temperamental son, Splinter tried to smile. "Come, Raphael. Let us come and see your brother."

Following his father closely, Raph tightened his wraps against his wrists. He had no right to complain about the pain, not with the amount of torture Donnie had been through. To be honest with himself, Raph felt bad about everybody else, but Donnie? Donnie was his brother.

He regretted all the things he did to him. Sitting on him, teasing him, messing up some of his experiments and blaming it on Mikey. It was he did to show how much he cared. But it was such a poor way of showing it...

Stepping through the door silently, Raphael tried to compose himself. An oxygen mask was held over his brother's face, tubes running up his arms, and a thick blanket covering his torso. His eyes were flickering, like he was dreaming.

"See Raphael? Your brother is resting. Your brother will be well."

Little whimpers started coming out of Donnie's mouth, his face contorting. His eyes were squeezed closed, tears dripping down from them. "No...this cannot be...my brothers..." The words were almost fragile, like they were coming from a million miles away. "This world...this...fut...nightmare...I won't ev...'bandon you..." Like mist disappearing into thin air, so did what Donnie was saying. He choked, his body going rigid, and it seemed like his eyes were rolling around in his skull.

And in just a moment, Raph was horrified. His brother began twitching, then shaking and convulsing. The movements were violent as foam began pouring out of Donatello's mouth. Rockwell was right by his side, yelling out at him, but he could hardly hear what he was saying.

Raph only knew one thing. His brother was dying, and there was nothing he could do about it.


	9. Donatello: A Nuclear of Memories

_**Different As It Always Will Be**_

 _ **Phase I:**_

 _ **Chapter Nine: A Nuclear of Memories**_

* * *

" _Donatello, my son..." The words were so calming, playing on a loop. "I understand that you cannot comprehend this, but I will prove it to you," It was his father's voice. Like all the times he had tried to reach out to him in meditation, where he could almost touch him. The closeness had always revitalized him, until that connection had been broken. His concentration, his focus, made it impossible. "You are safe. You have no need to worry," He wanted to believe him, he truly did. But how could he? It wasn't real. None of this was real. "You will learn this, but for now, you need to rest. Rest your mind, my son. Rest..." He wanted to reach out, to feel the embrace again, but just as soon as it was there, it was gone. It was real. It had been real. Everything else was a lie. What was he running from? He could not even remember. He just wanted his father. He felt like a child._

Cold air hit him in the face, and he cringed. He had known that it was a lie. He was back in his cell, waiting for what they would do next. The room was dark, like it always had been, but...it was different. He sensed that in an instant. The feel, the air, the smell. It was too cold. The air was stale. The smell...musty. Not like its rancid self.

Donnie was laying down, his flesh against cold metal. His hands, however, were not strapped down. What kind of trick were they playing this time? He rose, slowly, and breathed.

He didn't hurt. Not a single millimeter on his body hurt. Out of everything, that was the very first thing he noticed. How could he not? Pain had become his life. A horrible, destitute life. But just like that...it was gone. His eyes, they were adjusted, and in mere moments he could see clearly. It was still pitch black, but he could see. It was the infirmary, his home. Right across from him was his old desk, broken and battered, but crisp and clean. It seemed like it was the only thing left in here.

Something white caught his eye. It was a piece of paper. As he picked it up, he carefully read the words. "Don't forget. Never forget. Change the past, alter the future. This is your mission, inch by inch."

Images flashed before his eyes.

" _It was just a nightmare..."_

" _Guys, where am I?" He was drowning...drowning in a sea of emotions..._

" _Don? What happened to you?"_

" _I'm sorry...I have to know what is wrong with me..."_

" _I'm only going to say this once, so you better listen, and you better listen well." They were all together...together as a family...It was a promise he was bound to keep beyond any measure. They had seen him die...before their very eyes..._

" _Booyakasha!"_

" _My brothers, where are my brothers?" There was no remorse in his voice at all. He didn't know how to fight it._

" _We're brother, remember? Brothers forever."_

 _His torment had begun. It would kill him. It would destroy his family. Everything would go black...he needed help. Just for him. He was a monster...a monster of a brother back from the dead. He was taking the bet of his life, sacrificing everything. He would forever remain that monster. There would be no family of trust. It would be...a shock to all of their systems. Could they be a family forever?_

 _There was his struggle within. He knew the truth would always be a lie. That was why he could say all was well. He was actually against his family. All until his time would come...at the monster's bidding, of course. It would be his downfall. Not even his mutation day could fix that. His 16th? It was unlike any other. He would kill...it didn't matter who, as long as it was somebody. That was his twisted way. It was his way of convincing himself that he was trying to save lives. That he was truly treasured beyond measure. But it was all his fault...he would never have a family reunion. He would never be able to fix everything. He had to take them out...it was the only way...straight into the nonexistence. Never again. He would be prepared to fight. Maybe...maybe this was all a nightmare...the monster inside...it was his other choice. To have no more pain. It was finally time to say goodbye._

Donnie gasped, doubling over. Looking at himself, he cried. He was wearing a dark trench coat, and he fingered the dark purple bandana around his head. This was him. This is who he was going to be. He was going to do everything in his power not to do that...to not continue this unending cycle...the soul of him. The soul of a thousand Donatellos. A million. A billion. They were infinite. This...this had no beginning, and unless he did something, there would be no end. That was why he was here. Not to save his brothers in this universe, but to save them in the next. In his universe. In this Donatello's past, and in his present. In the nexus of reality, where everything hung in the balance.

"No. No! This cannot be...my brothers..." Donnie grimaced, gazing at the scars that littered his arms. So many were from his own kin. "This world. This future. It is a nightmare! I will never abandon you!" No one could hear him, he was certain, but he was crying out for them. For the ones he had strived so long to see again. To feel their warmth, their comfort, their love.

He heard it first. A blast, followed by so many more. The room shook, the dust stirring. The heat was becoming overwhelming, and the last thing Donatello was certain he saw was the blast of an explosion that could be described as nothing short of nuclear. His body was being ripped apart, and he knew he had purposefully done this. Not him...but the one who's body he inhabited. The breath he would no longer be. In an effort to erase the world he had created, he was killing everything. He was so desperate for it to end...for a new world to begin...he was willing to die for it.

He pushed him out. Mentally, not physically, he took over. It gave Donnie just the chance he needed to snap back where he was supposed to be.

* * *

 **A/N: For those wondering, all of those flashbacks are the title chapters of my previous Same As It Never Was Story, SAINWO. That plays a big key XD**


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